bioem.h

#ifndef BIOEM_H
#define BIOEM_H

#include "defs.h"
#include "bioem.h"
#include "model.h"
#include "map.h"
#include "param.h"

class bioem
{
	friend class bioem_RefMap;
	friend class bioem_Probability;

public:
	bioem();
	virtual ~bioem();

	int configure(int ac, char* av[]);
	void cleanup(); //Cleanup everything happening during configure

	int precalculate(); // Is it better to pass directly the input File names?
	int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
	int run();
	int doProjections(int iMap);
	int createConvolutedProjectionMap(int iOreint, int iMap, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC);

	virtual int compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);

	virtual void* malloc_device_host(size_t size);
	virtual void free_device_host(void* ptr);

	int createProjection(int iMap, mycomplex_t* map);
	int calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare);
	void calculateCCFFT(int iMap, int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC);

	bioem_Probability pProb;

        string OutfileName;
	bool yesoutfilename;


protected:
	virtual int deviceInit();
	virtual int deviceStartRun();
	virtual int deviceFinishRun();

	bioem_param param;
	bioem_model Model;
	bioem_RefMap RefMap;

	int nReferenceMaps;			//Maps in memory at a time
	int nReferenceMapsTotal;	//Maps in total

	int nProjectionMaps;		//Maps in memory at a time
	int nProjectionMapsTotal;	//Maps in total

	int FFTAlgo;				//Use the FFT Algorithm (Default 1)
	int DebugOutput;			//Debug Output Level (Default 2)
	int nProjectionsAtOnce;		//Number of projections to do at once via OpenMP (Default 1)
};

#endif